Nuclear Resonance Vibrational Spectroscopy Definition of O 2 Intermediates in an Extradiol Dioxygenase

Correlation to Crystallography and Reactivity

Kyle D. Sutherlin, Yuko Wasada-Tsutsui, Michael M. Mbughuni, Melanie Rogers, Kiyoung Park, Lei V. Liu, Yeonju Kwak, Martin Srnec, Lars H. Böttger, Mathieu Frenette, Yoshitaka Yoda, Yasuhiro Kobayashi, Masayuki Kurokuzu, Makina Saito, Makoto Seto, Michael Hu, Jiyong Zhao, E. Ercan Alp, John D Lipscomb, Edward I. Solomon

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O 2 . The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O 2 intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O 2 -4NC species and a Fe-O 2 -4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as Fe III -superoxo-catecholate and Fe III -peroxy-semiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of nonheme Fe-O 2 intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on Fe III -superoxo-catecholate and an end-on Fe III -hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a Fe III -hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of Fe III -superoxo and Fe III -hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.

Original languageEnglish (US)
Pages (from-to)16495-16513
Number of pages19
JournalJournal of the American Chemical Society
Volume140
Issue number48
DOIs
StatePublished - Dec 5 2018

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Vibrational spectroscopy
Crystallography
3,4-dihydroxyphenylacetate 2,3-dioxygenase
Spectrum Analysis
Enzymes
Electronic structure
Bioremediation
Protonation
Peroxides
Catechols
Catalysis
Hydrogen bonds
Environmental Biodegradation
extradiol dioxygenase
4-nitrocatechol
Hydrogen
Substrates

Cite this

Nuclear Resonance Vibrational Spectroscopy Definition of O 2 Intermediates in an Extradiol Dioxygenase : Correlation to Crystallography and Reactivity. / Sutherlin, Kyle D.; Wasada-Tsutsui, Yuko; Mbughuni, Michael M.; Rogers, Melanie; Park, Kiyoung; Liu, Lei V.; Kwak, Yeonju; Srnec, Martin; Böttger, Lars H.; Frenette, Mathieu; Yoda, Yoshitaka; Kobayashi, Yasuhiro; Kurokuzu, Masayuki; Saito, Makina; Seto, Makoto; Hu, Michael; Zhao, Jiyong; Alp, E. Ercan; Lipscomb, John D; Solomon, Edward I.

In: Journal of the American Chemical Society, Vol. 140, No. 48, 05.12.2018, p. 16495-16513.

Research output: Contribution to journalArticle

Sutherlin, KD, Wasada-Tsutsui, Y, Mbughuni, MM, Rogers, M, Park, K, Liu, LV, Kwak, Y, Srnec, M, Böttger, LH, Frenette, M, Yoda, Y, Kobayashi, Y, Kurokuzu, M, Saito, M, Seto, M, Hu, M, Zhao, J, Alp, EE, Lipscomb, JD & Solomon, EI 2018, 'Nuclear Resonance Vibrational Spectroscopy Definition of O 2 Intermediates in an Extradiol Dioxygenase: Correlation to Crystallography and Reactivity', Journal of the American Chemical Society, vol. 140, no. 48, pp. 16495-16513. https://doi.org/10.1021/jacs.8b06517
Sutherlin, Kyle D. ; Wasada-Tsutsui, Yuko ; Mbughuni, Michael M. ; Rogers, Melanie ; Park, Kiyoung ; Liu, Lei V. ; Kwak, Yeonju ; Srnec, Martin ; Böttger, Lars H. ; Frenette, Mathieu ; Yoda, Yoshitaka ; Kobayashi, Yasuhiro ; Kurokuzu, Masayuki ; Saito, Makina ; Seto, Makoto ; Hu, Michael ; Zhao, Jiyong ; Alp, E. Ercan ; Lipscomb, John D ; Solomon, Edward I. / Nuclear Resonance Vibrational Spectroscopy Definition of O 2 Intermediates in an Extradiol Dioxygenase : Correlation to Crystallography and Reactivity. In: Journal of the American Chemical Society. 2018 ; Vol. 140, No. 48. pp. 16495-16513.
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abstract = "The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O 2 . The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O 2 intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O 2 -4NC species and a Fe-O 2 -4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as Fe III -superoxo-catecholate and Fe III -peroxy-semiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of nonheme Fe-O 2 intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on Fe III -superoxo-catecholate and an end-on Fe III -hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a Fe III -hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of Fe III -superoxo and Fe III -hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.",
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T1 - Nuclear Resonance Vibrational Spectroscopy Definition of O 2 Intermediates in an Extradiol Dioxygenase

T2 - Correlation to Crystallography and Reactivity

AU - Sutherlin, Kyle D.

AU - Wasada-Tsutsui, Yuko

AU - Mbughuni, Michael M.

AU - Rogers, Melanie

AU - Park, Kiyoung

AU - Liu, Lei V.

AU - Kwak, Yeonju

AU - Srnec, Martin

AU - Böttger, Lars H.

AU - Frenette, Mathieu

AU - Yoda, Yoshitaka

AU - Kobayashi, Yasuhiro

AU - Kurokuzu, Masayuki

AU - Saito, Makina

AU - Seto, Makoto

AU - Hu, Michael

AU - Zhao, Jiyong

AU - Alp, E. Ercan

AU - Lipscomb, John D

AU - Solomon, Edward I.

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N2 - The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O 2 . The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O 2 intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O 2 -4NC species and a Fe-O 2 -4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as Fe III -superoxo-catecholate and Fe III -peroxy-semiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of nonheme Fe-O 2 intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on Fe III -superoxo-catecholate and an end-on Fe III -hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a Fe III -hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of Fe III -superoxo and Fe III -hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.

AB - The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O 2 . The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O 2 intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O 2 -4NC species and a Fe-O 2 -4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as Fe III -superoxo-catecholate and Fe III -peroxy-semiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of nonheme Fe-O 2 intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on Fe III -superoxo-catecholate and an end-on Fe III -hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a Fe III -hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of Fe III -superoxo and Fe III -hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.

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